Load the required libraries.
library(tidyverse)
library(sf)
library(here)
library(readxl)
library(scales)
library(DT)
library(brms)
library(tidybayes)
library(patchwork)
library(marginaleffects)
library(ggrepel)
library(scico)
library(ggdensity)
library(ggpubr)
library(units)
#library(ggsn)
Functions that we will use throughout the script
#labeller for years
year_labels <- c(1950:1963)
#The Glasgow mass minuture chest X-ray campaign happened between 11th March and 12th April 1957
#Segment for graphs to match ACF period
acf_start <- decimal_date(ymd("1957-03-11"))
acf_end <- decimal_date(ymd("1957-04-12"))
Function for counterfactual plots
if (length(facet_vars) != 0) {
p <- p + facet_wrap(facet_vars)
}
Error: object 'facet_vars' not found
Function for calculating measures of change over time (RR.peak, RR.level, RR.slope)
summarise_change <- function(model_data, model, population_denominator, grouping_var = NULL, re_formula = NULL) {
#functions for calculating RR.peak
#i.e. relative case notification rate in 1957 vs. counterfactual trend for 1957
grouping_var <- enquo(grouping_var)
if (!is.null({{grouping_var}})) {
#make the prediction matrix, conditional on whether we want random effects included or not.
out <- crossing({{model_data}} %>%
select({{population_denominator}}, y_num, !!grouping_var) %>%
filter(y_num == 8),
acf_period = c("a. pre-acf", "b. acf")
)
} else {
out <- crossing({{model_data}} %>%
select({{population_denominator}}, y_num) %>%
filter(y_num == 8),
acf_period = c("a. pre-acf", "b. acf")
)
}
peak_draws <- add_epred_draws(newdata = out,
object = {{model}},
re_formula = {{re_formula}}) %>%
mutate(epred_cnr = .epred/population_without_inst_ship*100000) %>%
group_by(.draw, !!grouping_var) %>%
summarise(estimate = last(epred_cnr)/first(epred_cnr)) %>%
ungroup() %>%
mutate(measure = "RR.peak")
peak_summary <- peak_draws %>%
group_by(!!grouping_var) %>%
mean_qi(estimate) %>%
mutate(measure = "RR.peak")
#functions for calculating RR.step
#i.e. relative case notification rate in 1958 vs. counterfactual trend for 1958
if (!is.null({{grouping_var}})) {
out2 <- crossing({{model_data}} %>%
select({{population_denominator}}, y_num, !!grouping_var) %>%
filter(y_num == 9),
acf_period = c("a. pre-acf", "c. post-acf")
)
} else {
out2 <- crossing({{model_data}} %>%
select({{population_denominator}}, y_num) %>%
filter(y_num == 9),
acf_period = c("a. pre-acf", "c. post-acf")
)
}
level_draws <- add_epred_draws(newdata = out2,
object = {{model}},
re_formula = {{re_formula}}) %>%
arrange(y_num, .draw) %>%
mutate(epred_cnr = .epred/population_without_inst_ship*100000) %>%
group_by(.draw, !!grouping_var) %>%
summarise(estimate = last(epred_cnr)/first(epred_cnr)) %>%
ungroup() %>%
mutate(measure = "RR.level")
level_summary <- level_draws %>%
group_by(!!grouping_var) %>%
mean_qi(estimate) %>%
mutate(measure = "RR.level")
#functions for calculating RR.slope
#i.e. relative change in case notification rate in 1958-1963 vs. counterfactual trend for 1959-1963
if (!is.null({{grouping_var}})) {
out3 <- crossing({{model_data}} %>%
select({{population_denominator}}, y_num, !!grouping_var) %>%
filter(y_num %in% c(9,14)),
acf_period = c("a. pre-acf", "c. post-acf")
)
} else {
out3 <- crossing({{model_data}} %>%
select({{population_denominator}}, y_num) %>%
filter(y_num %in% c(9,14)),
acf_period = c("a. pre-acf", "c. post-acf")
)
}
slope_draws <- add_epred_draws(newdata = out3,
object = {{model}},
re_formula = {{re_formula}}) %>%
arrange(y_num) %>%
ungroup() %>%
mutate(epred_cnr = .epred/population_without_inst_ship*100000) %>%
group_by(.draw, acf_period, !!grouping_var) %>%
summarise(slope = (last(epred_cnr) - first(epred_cnr)) / (last(y_num)-first(y_num))) %>%
ungroup() %>%
group_by(.draw, !!grouping_var) %>%
summarise(estimate = last(slope)/first(slope)) %>%
mutate(measure = "RR.slope")
slope_summary <- slope_draws %>%
group_by(!!grouping_var) %>%
median_qi(estimate) %>%
mutate(measure = "RR.slope")
#gather all the results into a named list
lst(peak_draws=peak_draws, peak_summary=peak_summary,
level_draws=level_draws, level_summary=level_summary,
slope_draws=slope_draws, slope_summary=slope_summary)
}
Function for calculating difference from counterfactual
calculate_counterfactual <- function(model_data, model, population_denominator, grouping_var=NULL, re_formula=NA){
#effect vs. counterfactual
counterfact <-
add_epred_draws(object = {{model}},
newdata = {{model_data}} %>%
select(year, year2, y_num, {{population_denominator}}, {{grouping_var}}) %>%
mutate(acf_period = "a. pre-acf"),
re_formula = {{re_formula}}) %>%
group_by(.draw, year, {{grouping_var}}, acf_period) %>%
mutate(.epred_inc_counterf = .epred/{{population_denominator}}*100000, .epred_counterf=.epred) %>%
filter(year>1957) %>%
ungroup() %>%
select(year, {{population_denominator}}, .draw, .epred_counterf, .epred_inc_counterf, {{grouping_var}})
#Calcuate case notification rate per draw, then summarise.
post_change <-
add_epred_draws(object = {{model}},
newdata = {{model_data}} %>%
select(year, year2, y_num, {{population_denominator}}, {{grouping_var}}, acf_period),
re_formula = {{re_formula}}) %>%
group_by(.draw, year, {{grouping_var}}, acf_period) %>%
mutate(.epred_inc = .epred/{{population_denominator}}*100000) %>%
filter(year>1957) %>%
ungroup() %>%
select(year, {{population_denominator}}, {{grouping_var}}, .draw, .epred, .epred_inc, {{grouping_var}})
#for the overall period
counterfact_overall <-
add_epred_draws(object = {{model}},
newdata = {{model_data}} %>%
select(year, year2, y_num, {{population_denominator}}, {{grouping_var}}) %>%
mutate(acf_period = "a. pre-acf"),
re_formula = {{re_formula}}) %>%
group_by(.draw, {{grouping_var}}) %>%
filter(year>1957) %>%
ungroup() %>%
select({{population_denominator}}, .draw, .epred, {{grouping_var}}) %>%
group_by(.draw, {{grouping_var}}) %>%
summarise(.epred_counterf = sum(.epred))
#Calcuate case notification rate per draw, then summarise.
post_change_overall <-
add_epred_draws(object = {{model}},
newdata = {{model_data}} %>%
select(year, year2, y_num, {{population_denominator}}, {{grouping_var}}, acf_period),
re_formula = {{re_formula}}) %>%
group_by(.draw, {{grouping_var}}) %>%
filter(year>1957) %>%
ungroup() %>%
select({{population_denominator}}, {{grouping_var}}, .draw, .epred) %>%
group_by(.draw, {{grouping_var}}) %>%
summarise(.epred = sum(.epred))
counter_post <-
left_join(counterfact, post_change) %>%
mutate(cases_averted = .epred_counterf-.epred,
pct_change = (.epred - .epred_counterf)/.epred_counterf,
diff_inc100k = .epred_inc - .epred_inc_counterf,
rr_inc100k = .epred_inc/.epred_inc_counterf) %>%
group_by(year, {{grouping_var}}) %>%
mean_qi(cases_averted, pct_change, diff_inc100k, rr_inc100k) %>%
ungroup()
counter_post_overall <-
left_join(counterfact_overall, post_change_overall) %>%
mutate(cases_averted = .epred_counterf-.epred,
pct_change = (.epred - .epred_counterf)/.epred_counterf) %>%
group_by({{grouping_var}}) %>%
mean_qi(cases_averted, pct_change) %>%
ungroup()
lst(counter_post, counter_post_overall)
}
Function for tidying up counterfactuals (mostly for making nice tables)
tidy_counterfactuals <- function(data){
data %>%
mutate(across(c(cases_averted:cases_averted.upper, diff_inc100k:diff_inc100k.upper), number_format(accuracy = 0.1, big.mark = ","))) %>%
mutate(across(c(rr_inc100k:rr_inc100k.upper), number_format(accuracy = 0.01))) %>%
mutate(across(c(pct_change:pct_change.upper), percent, accuracy=0.1)) %>%
mutate(year = as.character(year),
cases_averted = glue::glue("{cases_averted} ({cases_averted.lower} to {cases_averted.upper})"),
pct_change = glue::glue("{pct_change} ({pct_change.lower} to {pct_change.upper})"),
diff_inc = glue::glue("{diff_inc100k} ({diff_inc100k.lower} to {diff_inc100k.upper})"),
rr_inc = glue::glue("{rr_inc100k} ({rr_inc100k.lower} to {rr_inc100k.upper})"))
}
tidy_counterfactuals_overall <- function(data){
data %>%
mutate(across(c(cases_averted:cases_averted.upper), number_format(accuracy = 0.1, big.mark = ","))) %>%
mutate(across(c(pct_change:pct_change.upper), percent, accuracy=0.1)) %>%
mutate(year = as.character(year),
cases_averted = glue::glue("{cases_averted} ({cases_averted.lower} to {cases_averted.upper})"),
pct_change = glue::glue("{pct_change} ({pct_change.lower} to {pct_change.upper})"))
}
Import datasets for analysis
Make a map of Glasgow wards
glasgow_wards_1951 <- st_read(here("mapping/glasgow_wards_1951.geojson"))
Reading layer `glasgow_wards_1951' from data source
`/Users/petermacpherson/Dropbox/Projects/Historical TB ACF 2023-11-28/Work/analysis/glasgow-cxr/mapping/glasgow_wards_1951.geojson' using driver `GeoJSON'
Simple feature collection with 37 features and 3 fields
Geometry type: MULTIPOLYGON
Dimension: XY
Bounding box: xmin: -4.393502 ymin: 55.77464 xmax: -4.070411 ymax: 55.92814
Geodetic CRS: WGS 84
#read in Scotland boundary
scotland <- st_read(here("mapping/Scotland_boundary/Scotland boundary.shp"))
Reading layer `Scotland boundary' from data source
`/Users/petermacpherson/Dropbox/Projects/Historical TB ACF 2023-11-28/Work/analysis/glasgow-cxr/mapping/Scotland_boundary/Scotland boundary.shp'
using driver `ESRI Shapefile'
Simple feature collection with 1 feature and 1 field
Geometry type: MULTIPOLYGON
Dimension: XY
Bounding box: xmin: 5513 ymin: 530249 xmax: 470332 ymax: 1220302
Projected CRS: OSGB36 / British National Grid
#make a bounding box for Glasgow
bbox <- st_bbox(glasgow_wards_1951) |> st_as_sfc()
#plot scotland with a bounding box around the City of Glasgow
scotland_with_bbox <- ggplot() +
geom_sf(data = scotland, fill="antiquewhite") +
geom_sf(data = bbox, colour = "#C60C30", fill="antiquewhite") +
theme_void() +
theme(panel.border = element_rect(colour = "grey78", fill=NA, linewidth = 0.5),
panel.background = element_rect(fill = "#EAF7FA", size = 0.3))
Warning: The `size` argument of `element_rect()` is deprecated as of ggplot2 3.4.0.
Please use the `linewidth` argument instead.
#plot the wards
#note we tidy up some names to fit on map
glasgow_ward_map <- glasgow_wards_1951 %>%
mutate(ward = case_when(ward=="Shettleston and Tollcross" ~ "Shettleston and\nTollcross",
ward=="Partick (West)" ~ "Partick\n(West)",
ward=="Partick (East)" ~ "Partick\n(East)",
ward=="North Kelvin" ~ "North\nKelvin",
ward=="Kinning Park" ~ "Kinning\nPark",
TRUE ~ ward)) %>%
ggplot() +
geom_sf(aes(fill=division)) +
geom_sf_label(aes(label = ward), size=3, fill=NA, label.size = NA, colour="black") +
#scale_colour_identity() +
scale_fill_brewer(palette = "Set3", name="City of Glasgow Division") +
theme_grey() +
labs(x="",
y="",
fill="Division") +
theme(legend.position = "top",
panel.border = element_rect(colour = "grey78", fill=NA, linewidth = 0.5),
panel.background = element_rect(fill = "antiquewhite", size = 0.3),
panel.grid.major = element_line(color = "grey78")) +
guides(fill=guide_legend(title.position = "top", title.hjust = 0.5, title.theme = element_text(face="bold")))
#add the map of scotland as an inset
glasgow_ward_map + inset_element(scotland_with_bbox, 0.75, 0, 1, 0.4)
ggsave(here("figures/s1.png"), height=10, width = 12)
NA
NA
Calculate areas per geographical unit
sf_use_s2(FALSE) #https://github.com/r-spatial/sf/issues/1762
Spherical geometry (s2) switched off
glasgow_wards_1951 <- glasgow_wards_1951 %>%
mutate(area = st_area(glasgow_wards_1951))
glasgow_wards_1951$area_km <- units::set_units(glasgow_wards_1951$area, km^2)
Make division shape files, and calculate area (stopped working, need to fix!)
# glasgow_divisions_1951 <- glasgow_wards_1951 %>%
# group_by(division) %>%
# summarize(geometry = st_union(geometry)) %>%
# nngeo::st_remove_holes() %>%
# mutate(area = st_area(glasgow_divisions_1951))
#
# glasgow_divisions_1951$area_km <- units::set_units(glasgow_divisions_1951$area, km^2)
Load in the datasets for denonomiators, and check for consistency.
overall_pops <- read_xlsx(path = "2023-11-28_glasgow-acf.xlsx", sheet = "overall_population")
overall_pops %>%
mutate(across(where(is.numeric) & !(year), ~comma(.))) %>%
datatable()
#shift year to midpoint
overall_pops <- overall_pops %>%
mutate(year2 = year+0.5)
Note, we have three population estimates:
(Population in shipping is estimated from the 1951 census, so is the same for most years)
First, plot the total population
overall_pops %>%
ggplot() +
geom_area(aes(y=total_population, x=year2), alpha=0.5, colour = "mediumseagreen", fill="mediumseagreen") +
geom_point(aes(y=total_population, x=year2), colour = "mediumseagreen") +
geom_vline(aes(xintercept=acf_start), linetype=3) +
geom_vline(aes(xintercept=acf_end), linetype=3) +
scale_y_continuous(labels=comma) +
scale_x_continuous(labels = year_labels,
breaks = year_labels) +
labs(
title = "Glasgow Corporation: total population",
subtitle = "1950 to 1963",
x = "Year",
y = "Population",
caption = "Mid-year estimates\nMass miniature X-ray campaign period between dashed lines (11th March-12th April 1957)"
) +
theme_ggdist()
NA
NA
Now the population excluding institutionalised and shipping population
overall_pops %>%
ggplot() +
geom_area(aes(y=population_without_inst_ship, x=year2), alpha=0.5, colour = "purple", fill="purple") +
geom_point(aes(y=population_without_inst_ship, x=year2), colour = "purple") +
geom_vline(aes(xintercept=acf_start), linetype=3) +
geom_vline(aes(xintercept=acf_end), linetype=3) +
scale_y_continuous(labels=comma) +
scale_x_continuous(labels = year_labels,
breaks = year_labels) +
labs(
title = "Glasgow Corporation: population excluding institutionalised and shipping",
subtitle = "1950 to 1963",
x = "Year",
y = "Population",
caption = "Mid-year estimates\nMass miniature X-ray campaign period between dashed lines (11th March-12th April 1957)"
) +
theme_ggdist()
NA
NA
There are 5 Divisions containing 37 Wards in the Glasgow Corporation, with consistent boundaries over time.
#look-up table for divisions and wards
ward_lookup <- read_xlsx(path = "2023-11-28_glasgow-acf.xlsx", sheet = "divisions_wards")
ward_pops <- read_xlsx(path = "2023-11-28_glasgow-acf.xlsx", sheet = "ward_population")
ward_pops %>%
mutate(across(where(is.numeric) & !(year), ~comma(.))) %>%
datatable()
#shift year to midpoint
ward_pops <- ward_pops %>%
mutate(year2 = year+0.5)
#Get the Division population
division_pops <- ward_pops %>%
group_by(division, year) %>%
summarise(population_without_inst_ship = sum(population_without_inst_ship, na.rm = TRUE),
institutions = sum(institutions, na.rm = TRUE),
shipping = sum(shipping, na.rm = TRUE),
total_population = sum(total_population, na.rm = TRUE))
`summarise()` has grouped output by 'division'. You can override using the `.groups` argument.
division_pops %>%
mutate(across(where(is.numeric) & !(year), ~comma(.))) %>%
datatable()
NA
Plot the overall population by Division and Ward
division_pops %>%
mutate(year2 = year+0.5) %>%
ggplot() +
geom_area(aes(y=total_population, x=year2, colour=division, fill=division), alpha=0.8) +
geom_point(aes(y=total_population, x=year2, colour=division)) +
geom_vline(aes(xintercept=acf_start), linetype=3) +
geom_vline(aes(xintercept=acf_end), linetype=3) +
scale_y_continuous(labels=comma) +
facet_wrap(division~.) +
scale_x_continuous(labels = year_labels,
breaks = year_labels,
guide = guide_axis(angle = 90)) +
scale_fill_brewer(palette = "Set3", name = "") +
scale_colour_brewer(palette = "Set3", name = "") +
labs(
title = "Glasgow Corporation: total population by Division",
subtitle = "1950 to 1963",
x = "Year",
y = "Population",
caption = "Mid-year estimates\nMass miniature X-ray campaign period between dashed lines (11th March-12th April 1957)"
) +
theme_ggdist() +
theme(legend.position = "bottom")
NA
NA
ward_pops %>%
ggplot() +
geom_area(aes(y=total_population, x=year2, colour=division, fill=division), alpha=0.8) +
geom_point(aes(y=total_population, x=year2, colour=division)) +
geom_vline(aes(xintercept=acf_start), linetype=3) +
geom_vline(aes(xintercept=acf_end), linetype=3) +
scale_y_continuous(labels=comma) +
facet_wrap(ward~., ncol=6) +
scale_x_continuous(labels = year_labels,
breaks = year_labels,
guide = guide_axis(angle = 90)) +
scale_fill_brewer(palette = "Set3", name="Division") +
scale_colour_brewer(palette = "Set3", name = "Division") +
labs(
title = "Glasgow City: total population by Ward",
subtitle = "1950 to 1963",
x = "Year",
y = "Population",
caption = "Mid-year estimates\nMass miniature X-ray campaign period between dashed lines (11th March-12th April 1957)"
) +
theme_ggdist() +
theme(legend.position = "bottom")
ggsave(here("figures/s2.png"), height=10, width=12)
Approximately, how many person-years of follow-up do we have?
overall_pops %>%
ungroup() %>%
summarise(across(year, length, .names = "years"),
across(c(population_without_inst_ship, total_population), sum)) %>%
mutate(across(where(is.double), comma)) %>%
datatable()
NA
NA
Change in population by ward
ward_pops %>%
group_by(ward) %>%
summarise(pct_change_pop = (last(population_without_inst_ship) - first(population_without_inst_ship))/first(population_without_inst_ship)) %>%
mutate(pct_change_pop = percent(pct_change_pop)) %>%
arrange(pct_change_pop) %>%
datatable()
NA
NA
NA
Output population density by ward and divison for regression modelling
Wards first
(stopped working, need to fix)
# ward_covariates <- glasgow_wards_1951 %>%
# left_join(ward_pops) %>%
# mutate(people_per_km_sq = as.double(population_without_inst_ship/area_km))
#
# #plot it out
#
# ward_covariates %>%
# ggplot() +
# geom_sf(aes(fill=people_per_km_sq)) +
# facet_wrap(year~., ncol=7) +
# scale_fill_viridis_c(option="A") +
# theme(legend.position = "bottom",
# axis.text.x = element_text(angle = 45, hjust=1))
#
# ggsave(here("figures/ward_pop_density.png"), width=10)
#
# write_rds(ward_covariates, here("populations/ward_covariates.rds"))
Now divisions first
(stopped working, need to fix)
# division_covariates <- glasgow_divisions_1951 %>%
# left_join(division_pops) %>%
# mutate(people_per_km_sq = as.double(total_population/area_km))
#
# #plot it out
#
# division_covariates %>%
# ggplot() +
# geom_sf(aes(fill=people_per_km_sq)) +
# geom_sf_label(aes(label = division), size=3, fill=NA, label.size = NA, colour="black", family = "Segoe UI") +
# facet_wrap(year~., ncol=7) +
# scale_fill_viridis_c(option="G") +
# theme(legend.position = "bottom",
# axis.text.x = element_text(angle = 45, hjust=1))
#
# ggsave(here("figures/division_pop_density.png"), width=10)
#
# write_rds(division_covariates, here("populations/division_covariates.rds"))
age_sex <- read_xlsx(path = "2023-11-28_glasgow-acf.xlsx", sheet = "age_sex_population") %>%
pivot_longer(cols = c(male, female),
names_to = "sex")
#collapse down to smaller age groups to be manageable
age_sex <- age_sex %>%
ungroup() %>%
mutate(age = case_when(age == "0 to 4" ~ "00 to 04",
age == "5 to 9" ~ "05 to 14",
age == "10 to 14" ~ "05 to 14",
age == "15 to 19" ~ "15 to 24",
age == "20 to 24" ~ "15 to 24",
age == "25 to 29" ~ "25 to 34",
age == "30 to 34" ~ "25 to 34",
age == "35 to 39" ~ "35 to 44",
age == "40 to 44" ~ "35 to 44",
age == "45 to 49" ~ "45 to 59",
age == "50 to 54" ~ "45 to 59",
age == "55 to 59" ~ "45 to 59",
TRUE ~ "60 & up")) %>%
group_by(year, age, sex) %>%
mutate(value = sum(value)) %>%
ungroup()
m_age_sex <- lm(value ~ splines::ns(year, knots = 3)*age*sex, data = age_sex)
summary(m_age_sex)
Warning: essentially perfect fit: summary may be unreliable
Call:
lm(formula = value ~ splines::ns(year, knots = 3) * age * sex,
data = age_sex)
Residuals:
Min 1Q Median 3Q Max
-1.185e-10 0.000e+00 0.000e+00 0.000e+00 1.185e-10
Coefficients: (14 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 5.222e+04 2.040e-10 2.559e+14 <2e-16 ***
splines::ns(year, knots = 3)1 -8.043e+03 4.071e-10 -1.976e+13 <2e-16 ***
splines::ns(year, knots = 3)2 NA NA NA NA
age05 to 14 3.669e+04 2.499e-10 1.468e+14 <2e-16 ***
age15 to 24 -3.893e+03 2.499e-10 -1.558e+13 <2e-16 ***
age25 to 34 -3.996e+04 2.499e-10 -1.599e+14 <2e-16 ***
age35 to 44 -4.230e+04 2.499e-10 -1.693e+14 <2e-16 ***
age45 to 59 5.459e+04 2.356e-10 2.317e+14 <2e-16 ***
age60 & up 7.533e+04 2.204e-10 3.418e+14 <2e-16 ***
sexmale 3.374e+03 2.886e-10 1.169e+13 <2e-16 ***
splines::ns(year, knots = 3)1:age05 to 14 -1.863e+03 4.985e-10 -3.737e+12 <2e-16 ***
splines::ns(year, knots = 3)2:age05 to 14 NA NA NA NA
splines::ns(year, knots = 3)1:age15 to 24 7.533e+04 4.985e-10 1.511e+14 <2e-16 ***
splines::ns(year, knots = 3)2:age15 to 24 NA NA NA NA
splines::ns(year, knots = 3)1:age25 to 34 1.325e+05 4.985e-10 2.658e+14 <2e-16 ***
splines::ns(year, knots = 3)2:age25 to 34 NA NA NA NA
splines::ns(year, knots = 3)1:age35 to 44 1.380e+05 4.985e-10 2.769e+14 <2e-16 ***
splines::ns(year, knots = 3)2:age35 to 44 NA NA NA NA
splines::ns(year, knots = 3)1:age45 to 59 3.474e+03 4.700e-10 7.390e+12 <2e-16 ***
splines::ns(year, knots = 3)2:age45 to 59 NA NA NA NA
splines::ns(year, knots = 3)1:age60 & up -8.453e+04 4.397e-10 -1.923e+14 <2e-16 ***
splines::ns(year, knots = 3)2:age60 & up NA NA NA NA
splines::ns(year, knots = 3)1:sexmale -1.994e+03 5.757e-10 -3.464e+12 <2e-16 ***
splines::ns(year, knots = 3)2:sexmale NA NA NA NA
age05 to 14:sexmale 1.053e+04 3.534e-10 2.980e+13 <2e-16 ***
age15 to 24:sexmale 2.352e+04 3.534e-10 6.656e+13 <2e-16 ***
age25 to 34:sexmale 1.355e+04 3.534e-10 3.833e+13 <2e-16 ***
age35 to 44:sexmale -1.727e+03 3.534e-10 -4.888e+12 <2e-16 ***
age45 to 59:sexmale 2.774e+03 3.332e-10 8.324e+12 <2e-16 ***
age60 & up:sexmale -7.761e+04 3.117e-10 -2.490e+14 <2e-16 ***
splines::ns(year, knots = 3)1:age05 to 14:sexmale -2.049e+04 7.051e-10 -2.906e+13 <2e-16 ***
splines::ns(year, knots = 3)2:age05 to 14:sexmale NA NA NA NA
splines::ns(year, knots = 3)1:age15 to 24:sexmale -6.780e+04 7.051e-10 -9.616e+13 <2e-16 ***
splines::ns(year, knots = 3)2:age15 to 24:sexmale NA NA NA NA
splines::ns(year, knots = 3)1:age25 to 34:sexmale -3.804e+04 7.051e-10 -5.396e+13 <2e-16 ***
splines::ns(year, knots = 3)2:age25 to 34:sexmale NA NA NA NA
splines::ns(year, knots = 3)1:age35 to 44:sexmale -1.171e+04 7.051e-10 -1.661e+13 <2e-16 ***
splines::ns(year, knots = 3)2:age35 to 44:sexmale NA NA NA NA
splines::ns(year, knots = 3)1:age45 to 59:sexmale -3.473e+04 6.647e-10 -5.224e+13 <2e-16 ***
splines::ns(year, knots = 3)2:age45 to 59:sexmale NA NA NA NA
splines::ns(year, knots = 3)1:age60 & up:sexmale 1.056e+05 6.218e-10 1.698e+14 <2e-16 ***
splines::ns(year, knots = 3)2:age60 & up:sexmale NA NA NA NA
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 3.074e-11 on 44 degrees of freedom
Multiple R-squared: 1, Adjusted R-squared: 1
F-statistic: 6.006e+29 on 27 and 44 DF, p-value: < 2.2e-16
age_levels <- age_sex %>% select(age) %>% distinct() %>% pull()
age_sex_nd <-
crossing(
age=age_levels,
sex=c("male", "female"),
year = 1950:1963
)
pred_pops <- age_sex_nd %>% modelr::add_predictions(m_age_sex)
Warning: prediction from a rank-deficient fit may be misleading
pred_pops %>%
ggplot(aes(x=year, y=pred, colour=age)) +
geom_line() +
geom_point() +
facet_grid(sex~.) +
scale_y_continuous(labels = comma, limits = c(0, 125000))
#How well do they match up with our overall populations?
pred_pops %>%
group_by(year) %>%
summarise(sum_pred_pop = sum(pred)) %>%
right_join(overall_pops) %>%
select(year, sum_pred_pop, population_without_inst_ship, total_population) %>%
pivot_longer(cols = c(sum_pred_pop, population_without_inst_ship, total_population)) %>%
ggplot(aes(x=year, y=value, colour=name)) +
geom_point() +
scale_y_continuous(labels = comma, limits = c(800000, 1250000))
Joining with `by = join_by(year)`
pred_pops %>%
group_by(year, sex) %>%
summarise(sum = sum(pred)) %>%
group_by(year) %>%
mutate(sex_ratio = first(sum)/last(sum))
`summarise()` has grouped output by 'year'. You can override using the `.groups` argument.
What percentage of adults (15+ participated in the intervention in 1957)?
pred_pops %>%
ungroup() %>%
filter(year==1957) %>%
filter(age != "00 to 04",
age != "05 to 14") %>%
summarise(total_pop = sum(pred)) %>%
mutate(cxr_screened = 622349) %>%
mutate(pct_pop_cxr_screened = percent(cxr_screened/total_pop))
pred_pops %>%
ungroup() %>%
filter(year==1957) %>%
filter(age != "00 to 04",
age != "05 to 14") %>%
summarise(total_pop = sum(pred), .by=sex) %>%
mutate(cxr_screened = c(340474, 281875)) %>%
mutate(pct_pop_cxr_screened = percent(cxr_screened/total_pop))
NA
NA
Population pyramids
label_abs <- function(x) {
comma(abs(x))
}
pred_pops %>%
ungroup() %>%
group_by(year) %>%
mutate(year_pop = sum(pred),
age_sex_pct = percent(pred/year_pop, accuracy=0.1)) %>%
mutate(sex = case_when(sex=="male" ~ "Male",
sex=="female" ~ "Female")) %>%
ggplot(
aes(x = age, fill = sex,
y = ifelse(test = sex == "Female",yes = -pred, no = pred))) +
geom_bar(stat = "identity") +
geom_text(aes(label = age_sex_pct),
position= position_stack(vjust=0.5), colour="white", size=2.5) +
facet_wrap(year~., ncol=7) +
coord_flip() +
scale_y_continuous(labels = label_abs) +
scale_fill_manual(values = c("mediumseagreen", "purple"), name="") +
theme_ggdist() +
theme(axis.text.x = element_text(angle=90, hjust = 1, vjust=0.5),
legend.position = "bottom",
panel.border = element_rect(colour = "grey78", fill=NA)) +
labs(x="", y="")
ggsave(here("figures/s3.png"), width=10)
Saving 10 x 4.5 in image
Not perfect, but resonably good. But ahhhhh… the age groups don’t align with the case notification age groups! Come back to think about this later.
Import the tuberculosis cases dataset
Overall, by year.
cases_by_year <- read_xlsx("2023-11-28_glasgow-acf.xlsx", sheet = "by_year")
cases_by_year%>%
mutate(across(where(is.numeric) & !(year), ~comma(.))) %>%
datatable()
#shift year to midpoint
cases_by_year <- cases_by_year %>%
mutate(year2 = year+0.5)
Plot the overall number of case notified per year, by pulmonary and extra pulmonary classification.
cases_by_year %>%
select(-total_notifications, -year) %>%
pivot_longer(cols = c(pulmonary_notifications, `non-pulmonary_notifications`)) %>%
mutate(name = case_when(name == "pulmonary_notifications" ~ "Pulmonary TB",
name == "non-pulmonary_notifications" ~ "Extra-pulmonary TB")) %>%
ggplot() +
geom_area(aes(y=value, x=year2, group = name, fill=name), alpha=0.5) +
geom_vline(aes(xintercept=acf_start), linetype=3) +
geom_vline(aes(xintercept=acf_end), linetype=3) +
scale_y_continuous(labels=comma) +
scale_x_continuous(labels = year_labels,
breaks = year_labels) +
scale_fill_brewer(palette = "Set1", name="") +
labs(
title = "Glasgow Corporation: Tuberculosis notifications",
subtitle = "1950 to 1963, by TB disease classification",
x = "Year",
y = "Number of cases",
caption = "Mass miniature X-ray campaign period between dashed lines (11th March-12th April 1957)"
) +
theme_ggdist() +
theme(legend.position = "bottom")
NA
NA
Read in the datasets and merge together.
#list all the sheets
all_sheets <- excel_sheets("2023-11-28_glasgow-acf.xlsx")
#get the ward sheets
ward_sheets <- enframe(all_sheets) %>%
filter(grepl("by_ward", value)) %>%
pull(value)
cases_by_ward_sex_year <- map_df(ward_sheets, ~read_xlsx(path = "2023-11-28_glasgow-acf.xlsx",
sheet = .))
cases_by_ward_sex_year %>%
mutate(across(where(is.numeric) & !(year), ~comma(.))) %>%
datatable()
NA
Aggregate together to get cases by division
cases_by_division <- cases_by_ward_sex_year %>%
left_join(ward_lookup) %>%
group_by(division, year, tb_type) %>%
summarise(cases = sum(cases, na.rm = TRUE))
Joining with `by = join_by(ward)``summarise()` has grouped output by 'division', 'year'. You can override using the `.groups` argument.
#shift year to midpoint
cases_by_division <- cases_by_division %>%
mutate(year2 = year+0.5) %>%
ungroup()
cases_by_division %>%
select(-year2) %>%
select(year, everything()) %>%
mutate(across(where(is.numeric) & !(year), ~comma(.))) %>%
datatable()
cases_by_division %>%
mutate(tb_type = case_when(tb_type == "Pulmonary" ~ "Pulmonary TB",
tb_type == "Non-Pulmonary" ~ "Extra-pulmonary TB")) %>%
ggplot() +
geom_area(aes(y=cases, x=year2, group = tb_type, fill=tb_type), alpha=0.5) +
geom_vline(aes(xintercept=acf_start), linetype=3) +
geom_vline(aes(xintercept=acf_end), linetype=3) +
scale_y_continuous(labels=comma) +
scale_x_continuous(labels = year_labels,
breaks = year_labels,
guide = guide_axis(angle = 90)) +
facet_wrap(division~., scales = "free_y") +
scale_fill_brewer(palette = "Set1", name="") +
labs(
title = "Glasgow Corporation: Tuberculosis notifications by Division",
subtitle = "1950 to 1963, by TB disease classification",
x = "Year",
y = "Number of cases",
caption = "Mass miniature X-ray campaign period between dashed lines (11th March-12th April 1957)\nNote: extra-pulmonary TB cases by Division/Ward not reported in 1962-1963"
) +
theme_ggdist() +
theme(legend.position = "bottom")
cases_by_ward <- cases_by_ward_sex_year %>%
group_by(ward, year, tb_type) %>%
summarise(cases = sum(cases, na.rm = TRUE)) %>%
ungroup()
`summarise()` has grouped output by 'ward', 'year'. You can override using the `.groups` argument.
cases_by_ward %>%
mutate(across(where(is.numeric) & !(year), ~comma(.))) %>%
select(year, everything()) %>%
datatable()
#shift year to midpoint
cases_by_ward <- cases_by_ward %>%
mutate(year2 = year+0.5)
cases_by_ward %>%
mutate(tb_type = case_when(tb_type == "Pulmonary" ~ "Pulmonary TB",
tb_type == "Non-Pulmonary" ~ "Extra-pulmonary TB")) %>%
ggplot() +
geom_area(aes(y=cases, x=year2, group = tb_type, fill=tb_type), alpha=0.8) +
geom_vline(aes(xintercept=acf_start), linetype=3) +
geom_vline(aes(xintercept=acf_end), linetype=3) +
scale_y_continuous(labels=comma) +
scale_x_continuous(labels = year_labels,
breaks = year_labels,
guide = guide_axis(angle = 90)) +
facet_wrap(ward~., scales = "free_y") +
scale_fill_brewer(palette = "Set1", name="") +
labs(
title = "Glasgow Corporation: Tuberculosis notifications by Ward",
subtitle = "1950 to 1963, by TB disease classification",
x = "Year",
y = "Number of cases",
caption = "Mass miniature X-ray campaign period between dashed lines (11th March-12th April 1957)\nNote: extra-pulmonary TB cases by Division/Ward not reported in 1962-1963"
) +
theme(legend.position = "bottom")
NA
NA
As we don’t have denominators, we will just model the change in counts.
#list all the sheets
all_sheets <- excel_sheets("2023-11-28_glasgow-acf.xlsx")
#get the ward sheets
age_sex_sheets <- enframe(all_sheets) %>%
filter(grepl("by_age_sex", value)) %>%
pull(value)
cases_by_age_sex <- map_df(age_sex_sheets, ~read_xlsx(path = "2023-11-28_glasgow-acf.xlsx",
sheet = .))
cases_by_age_sex %>%
mutate(across(where(is.numeric) & !(year), ~comma(.))) %>%
datatable()
NA
NA
Now calculate case notification rates per 100,000 population
Merge the notification and population denominator datasets together.
Here we need to include the whole population (with shipping and institutions) as they are included in the notifications.
overall_inc <- overall_pops %>%
left_join(cases_by_year)
Joining with `by = join_by(year, year2)`
overall_inc <- overall_inc %>%
mutate(inc_pulm_100k = pulmonary_notifications/total_population*100000,
inc_ep_100k = `non-pulmonary_notifications`/total_population*100000,
inc_100k = total_notifications/total_population*100000)
overall_inc %>%
select(year, inc_100k, inc_pulm_100k, inc_ep_100k) %>%
mutate_at(.vars = vars(inc_100k, inc_pulm_100k, inc_ep_100k),
.funs = funs(round)) %>%
datatable()
Warning: `funs()` was deprecated in dplyr 0.8.0.
Please use a list of either functions or lambdas:
# Simple named list:
list(mean = mean, median = median)
# Auto named with `tibble::lst()`:
tibble::lst(mean, median)
# Using lambdas
list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
overall_inc %>%
select(year2, inc_pulm_100k, inc_ep_100k) %>%
pivot_longer(cols = c(inc_pulm_100k, `inc_ep_100k`)) %>%
mutate(name = case_when(name == "inc_pulm_100k" ~ "Pulmonary TB",
name == "inc_ep_100k" ~ "Extra-pulmonary TB")) %>%
ggplot() +
geom_area(aes(y=value, x=year2, group = name, fill=name), alpha=0.5) +
geom_vline(aes(xintercept=acf_start), linetype=3) +
geom_vline(aes(xintercept=acf_end), linetype=3) +
scale_y_continuous(labels=comma) +
scale_x_continuous(labels = year_labels,
breaks = year_labels) +
scale_fill_brewer(palette = "Set1", name="") +
labs(
title = "Glasgow Corporation: Tuberculosis case notification rate",
subtitle = "1950 to 1963, by TB disease classification",
x = "Year",
y = "Case notification rate (per 100,000)",
caption = "Mass miniature X-ray campaign period between dashed lines (11th March-12th April 1957)"
) +
theme_ggdist() +
theme(legend.position = "bottom")
NA
NA
NA
division_inc <- division_pops %>%
left_join(cases_by_division)
Joining with `by = join_by(division, year)`
division_inc <- division_inc %>%
mutate(inc_100k = cases/total_population*100000)
division_inc %>%
select(year, division, tb_type, inc_100k) %>%
mutate_at(.vars = vars(inc_100k),
.funs = funs(round)) %>%
datatable()
Warning: `funs()` was deprecated in dplyr 0.8.0.
Please use a list of either functions or lambdas:
# Simple named list:
list(mean = mean, median = median)
# Auto named with `tibble::lst()`:
tibble::lst(mean, median)
# Using lambdas
list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
division_inc %>%
mutate(tb_type = case_when(tb_type == "Pulmonary" ~ "Pulmonary TB",
tb_type == "Non-Pulmonary" ~ "Extra-pulmonary TB")) %>%
ggplot() +
geom_area(aes(y=inc_100k, x=year2, group = tb_type, fill=tb_type), alpha=0.5) +
geom_vline(aes(xintercept=acf_start), linetype=3) +
geom_vline(aes(xintercept=acf_end), linetype=3) +
scale_y_continuous(labels=comma) +
scale_x_continuous(labels = year_labels,
breaks = year_labels,
guide = guide_axis(angle = 90)) +
facet_wrap(division~.) +
scale_fill_brewer(palette = "Set1", name="") +
labs(
title = "Glasgow Corporation: Tuberculosis case notification rate, by Division",
subtitle = "1950 to 1963, by TB disease classification",
x = "Year",
y = "Case notification rate (per 100,000)",
caption = "Mass miniature X-ray campaign period between dashed lines (11th March-12th April 1957)\nNote: extra-pulmonary TB cases by Division/Ward not reported in 1962-1963"
) +
theme_ggdist() +
theme(legend.position = "bottom")
NA
NA
NA
Here we will filter out the institutions and harbour from the denominators, as we don’t have reliable population denominators for them.
ward_inc <- ward_pops %>%
left_join(cases_by_ward)
Joining with `by = join_by(ward, year, year2)`
ward_inc <- ward_inc %>%
mutate(inc_100k = cases/population_without_inst_ship*100000)
ward_inc %>%
select(year, ward, tb_type, inc_100k) %>%
mutate_at(.vars = vars(inc_100k),
.funs = funs(round)) %>%
datatable()
Warning: `funs()` was deprecated in dplyr 0.8.0.
Please use a list of either functions or lambdas:
# Simple named list:
list(mean = mean, median = median)
# Auto named with `tibble::lst()`:
tibble::lst(mean, median)
# Using lambdas
list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
ward_inc %>%
mutate(tb_type = case_when(tb_type == "Pulmonary" ~ "Pulmonary TB",
tb_type == "Non-Pulmonary" ~ "Extra-pulmonary TB")) %>%
ggplot() +
geom_area(aes(y=inc_100k, x=year2, group = tb_type, fill=tb_type), alpha=0.5) +
geom_vline(aes(xintercept=acf_start), linetype=3) +
geom_vline(aes(xintercept=acf_end), linetype=3) +
scale_y_continuous(labels=comma) +
scale_x_continuous(labels = year_labels,
breaks = year_labels,
guide = guide_axis(angle = 90)) +
facet_wrap(ward~.) +
scale_fill_brewer(palette = "Set1", name="") +
labs(
title = "Glasgow Corporation: Tuberculosis case notification rate, by Ward",
subtitle = "1950 to 1963, by TB disease classification",
x = "Year",
y = "Incidence (per 100,000)",
caption = "Mass miniature X-ray campaign period between dashed lines (11th March-12th April 1957)\nNote: extra-pulmonary TB cases by Division/Ward not reported in 1962-1963"
) +
theme(legend.position = "bottom")
NA
NA
NA
NA
On a map
st_as_sf(left_join(ward_inc, glasgow_wards_1951)) %>%
filter(tb_type=="Pulmonary") %>%
ggplot() +
geom_sf(aes(fill=inc_100k)) +
facet_wrap(year~., ncol = 7) +
scale_fill_viridis_c(name="Case notification rate (per 100,000)",
option = "A") +
theme_ggdist() +
theme(legend.position = "top",
legend.key.width = unit(2, "cm"),
panel.border = element_rect(colour = "grey78", fill=NA)) +
guides(fill=guide_colorbar(title.position = "top"))
Joining with `by = join_by(division, ward, ward_number)`
Import the TB mortality data.
First, overall deaths. Note that in the original reports, we have a pulmonary TB death rate per million for all years, and numbers of pulmonary TB deaths for each year apart from 1950.
#get the overall mortality sheets
deaths_sheets <- enframe(all_sheets) %>%
filter(grepl("deaths", value)) %>%
pull(value)
overall_deaths <- map_df(deaths_sheets, ~read_xlsx(path = "2023-11-28_glasgow-acf.xlsx",
sheet = .))
overall_deaths %>%
mutate(across(where(is.numeric) & !(year), ~comma(.))) %>%
datatable()
NA
NA
NA
Plot the raw numbers of pulmonary deaths
overall_deaths %>%
ggplot(aes(x=year, y=pulmonary_deaths)) +
geom_line(colour = "#DE0D92") +
geom_point(colour = "#DE0D92") +
geom_vline(aes(xintercept=acf_start), linetype=3) +
geom_vline(aes(xintercept=acf_end), linetype=3) +
labs(y="Pulmonary TB deaths per year",
x = "Year",
title = "Numbers of pulmonary TB deaths",
subtitle = "Glasgow, 1950-1963",
caption = "Mass miniature X-ray campaign period between dashed lines (11th March-12th April 1957)\nNote: no data for 1950") +
theme_ggdist() +
theme(panel.border = element_rect(colour = "grey78", fill=NA))
NA
NA
Now the incidence of pulmonary TB death
overall_deaths %>%
ggplot(aes(x=year, y=pulmonary_death_rate_per_100k)) +
geom_line(colour = "#4D6CFA") +
geom_point(colour = "#4D6CFA") +
geom_vline(aes(xintercept=acf_start), linetype=3) +
geom_vline(aes(xintercept=acf_end), linetype=3) +
scale_y_continuous(labels=comma) +
scale_x_continuous(labels = year_labels,
breaks = year_labels) +
labs(y="Annual incidence of death (per 100,000)",
x = "Year",
caption = "Mass miniature X-ray campaign period between dashed lines (11th March-12th April 1957)") +
theme_ggdist() +
theme(panel.border = element_rect(colour = "grey78", fill=NA))
ggsave(here("figures/s7.png"), width=10)
Saving 10 x 4.5 in image
Make Table 1 here, and save for publication.
overall_pops %>%
select(year, total_population) %>%
left_join(overall_inc %>%
select(year,
pulmonary_notifications, inc_pulm_100k,
`non-pulmonary_notifications`, inc_ep_100k,
total_notifications, inc_100k)) %>%
left_join(overall_deaths %>%
select(year,
pulmonary_deaths, pulmonary_death_rate_per_100k)) %>%
mutate(across(where(is.numeric) & !(year), ~round(., digits=1))) %>%
mutate(across(where(is.numeric) & !(year), ~comma(.)))
Joining with `by = join_by(year)`Joining with `by = join_by(year)`
Prepare the datasets for modelling
mdata <- ward_inc %>%
filter(tb_type=="Pulmonary") %>%
mutate(acf_period = case_when(year %in% c(1950:1956) ~ "a. pre-acf",
year %in% c(1957) ~ "b. acf",
year %in% c(1958:1963) ~ "c. post-acf")) %>%
group_by(ward) %>%
mutate(y_num = row_number()) %>%
ungroup()
mdata_extrapulmonary <- ward_inc %>%
filter(tb_type=="Non-Pulmonary") %>%
mutate(acf_period = case_when(year %in% c(1950:1956) ~ "a. pre-acf",
year %in% c(1957) ~ "b. acf",
year %in% c(1958:1963) ~ "c. post-acf")) %>%
group_by(ward) %>%
mutate(y_num = row_number()) %>%
ungroup()
#scaffold for overall predictions
overall_scaffold <- mdata %>%
select(year, year2, y_num, acf_period, population_without_inst_ship, ward, cases) %>%
group_by(year, year2, y_num, acf_period) %>%
summarise(population_without_inst_ship = sum(population_without_inst_ship),
cases = sum(cases)) %>%
ungroup() %>%
mutate(inc_100k = cases/population_without_inst_ship*100000) %>%
left_join(mdata_extrapulmonary %>% group_by(year) %>%
summarise(cases_extrapulmonary = sum(cases))) %>%
mutate(inc_100k_extrapulmonary = cases_extrapulmonary/population_without_inst_ship*100000)
`summarise()` has grouped output by 'year', 'year2', 'y_num'. You can override using the `.groups` argument.Joining with `by = join_by(year)`
This models the case notification rate over time, with a step change for the intervention, and slope change after the intervention.
Work on the priors a bit. We will build up from less complex to more complex.
at the intercept, we expect somewhere around 2500. We will set the standard deviation to both 0.5 and 1 to check what it looks like
c(prior(lognormal(7.600902, 0.5)), #log(2500) = 7.600902
prior(lognormal(7.600902, 1))) %>%
parse_dist() %>%
ggplot(aes(y = prior, dist = .dist, args = .args)) +
stat_halfeye(.width = c(.5, .95)) +
scale_y_discrete(NULL, labels = str_c("lognormal(log(2000), ", c(0.5, 1), ")"),
expand = expansion(add = 0.1)) +
xlab(expression(exp(italic(p)(beta[0])))) +
coord_cartesian(xlim = c(0,15000))
prior(gamma(1, 0.01)) %>%
parse_dist() %>%
ggplot(aes(y=prior, dist = .dist, args = .args)) +
stat_halfeye(.width = c(0.5, 0.95))
#now fit to a model, and plot some prior realisations
m_prior1 <- brm(
cases ~ 0 + Intercept,
family = negbinomial(),
data = overall_scaffold,
sample_prior = "only",
prior = prior(normal(log(2000), 0.5), class = b, coef = Intercept) +
prior(gamma(1, 0.01), class = shape)
)
Compiling Stan program...
Start sampling
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 1.3e-05 seconds
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add_epred_draws(object=m_prior1,
newdata = tibble(intercept=1)) %>%
ggplot(aes(x=intercept, y=.epred)) +
stat_halfeye() +
scale_y_log10(labels = comma)
NA
NA
Now try to add in a term for the effect of y_num. We anticpate that the number of cases will decline by about 1-5% per year. However, as we are pretty uncertain about this, we will just encode a weakly regularising prior to restrict the year size to sensible ranges.
m_prior2 <- brm(
cases ~ 0 + Intercept + y_num,
family = negbinomial(),
data = overall_scaffold,
sample_prior = "only",
prior = prior(normal(log(2000), 0.5), class = b, coef = Intercept) +
prior(gamma(1, 0.01), class = shape) +
prior(normal(0, 0.01), class = b, coef = y_num)
)
Compiling Stan program...
Start sampling
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 1).
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add_epred_draws(object=m_prior2,
newdata = overall_scaffold) %>%
ggplot(aes(x=year, y=.epred)) +
stat_halfeye() +
scale_y_log10(label=comma)
Now we want to add in a prior for the effect of the acf_intervention. We anticipate the peak to be anywhere between no effect, and a tripling
m_prior3 <- brm(
cases ~ 0 + Intercept + y_num + acf_period,
family = negbinomial(),
data = overall_scaffold,
sample_prior = "only",
prior = prior(normal(log(2000), 0.5), class = b, coef = Intercept) +
prior(gamma(1, 0.01), class = shape) +
prior(normal(0, 0.01), class = b, coef = y_num) +
prior(normal(0, 0.001), class = b)
)
Compiling Stan program...
Start sampling
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 1).
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add_epred_draws(object=m_prior3,
newdata = overall_scaffold) %>%
ggplot(aes(x=year, y=.epred)) +
stat_halfeye() +
scale_y_log10(labels = comma)
NA
NA
NA
Now we look and see what it looks like with the interactions
m_prior4 <- brm(
cases ~ 0 + Intercept + y_num + acf_period + y_num:acf_period,
family = negbinomial(),
data = overall_scaffold,
sample_prior = "only",
prior = prior(normal(log(2500), 1), class = b, coef = Intercept) +
prior(gamma(1, 0.01), class = shape) +
prior(normal(0, 0.01), class = b)
)
Compiling Stan program...
Start sampling
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 1).
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add_epred_draws(object=m_prior4,
newdata = overall_scaffold) %>%
ggplot(aes(x=year, y=.epred)) +
stat_halfeye() +
scale_y_log10(label=comma)
NA
NA
NA
Now try adding in the random intercepts
c(prior(lognormal(3.912023, 0.5)), #log(50) = 3.912023
prior(lognormal(3.912023, 1))) %>%
parse_dist() %>%
ggplot(aes(y = prior, dist = .dist, args = .args)) +
stat_halfeye(.width = c(.5, .95)) +
scale_y_discrete(NULL, labels = str_c("lognormal(log(50), ", c(0.5, 1), ")"),
expand = expansion(add = 0.1)) +
xlab(expression(exp(italic(p)(beta[0])))) +
coord_cartesian(xlim = c(0,400))
m_prior5 <- brm(
cases ~ y_num + acf_period + y_num:acf_period + ( 1 | ward),
family = negbinomial(),
data = mdata,
sample_prior = "only",
prior = prior(normal(log(50), 1), class = Intercept) +
prior(gamma(1, 0.01), class = shape) +
prior(normal(0, 0.01), class = b) +
prior(exponential(1), class=sd)
)
Compiling Stan program...
Start sampling
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 1).
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add_epred_draws(object=m_prior5,
newdata = mdata,
re_formula = NA) %>%
ggplot(aes(x=year, y=.epred)) +
stat_halfeye() +
scale_y_log10(label=comma)
add_epred_draws(object=m_prior5,
newdata = mdata,
re_formula = NA) %>%
ggplot(aes(x=year, y=.epred)) +
stat_halfeye() +
scale_y_log10(label=comma) +
facet_wrap(ward~.)
And add in the random slopes
m_prior6 <- brm(
cases ~ 1 + y_num + acf_period + y_num:acf_period + (1 + y_num*acf_period | ward),
family = negbinomial(),
data = mdata,
sample_prior = "only",
prior = prior(gamma(1, 0.01), class = shape) +
prior(normal(0, 0.1), class = b) +
prior(exponential(1), class=sd) +
prior(lkj(2), class=cor)
)
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m_prior6 <- brm(
cases ~ 0 + Intercept + y_num + acf_period + y_num:acf_period + ( y_num*acf_period | ward),
family = negbinomial(),
data = mdata,
sample_prior = "only",
prior = prior(normal(log(50), 1), class = b, coef = Intercept) +
prior(gamma(1, 0.01), class = shape) +
prior(normal(0, 0.01), class = b) +
prior(exponential(100), class=sd) +
prior(lkj(2), class=cor)
)
Compiling Stan program...
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add_epred_draws(object=m_prior6,
newdata = mdata,
re_formula = NA) %>%
ggplot(aes(x=year, y=.epred)) +
stat_halfeye() +
scale_y_log10(label=comma)
add_epred_draws(object=m_prior6,
newdata = mdata,
re_formula = ~( 1 + y_num + acf_period | ward)) %>%
ggplot(aes(x=year, y=.epred)) +
stat_halfeye() +
scale_y_log10(label=comma) +
facet_wrap(ward~.)
plot_counterfactual(model_data = overall_scaffold, model=m_prior6, outcome = inc_100k,
population_denominator = population_without_inst_ship, re_formula = NA)
plot_counterfactual(model_data = mdata, model=m_prior6, outcome = inc_100k,
population_denominator = population_without_inst_ship, grouping_var = ward, ward,
re_formula = ~( 1 + y_num + acf_period | ward))
Issue here is the non-centred parameterisation of the intercept prior… Feel like this is a more interpretable way to set priors… but will revert to centred parameterisation for the meantime.
Look at the mean and variance of counts (counts of pulmonary notifications are what we are predicting)
#Mean of counts per year
mean(mdata$cases)
[1] 48.32819
#variance of counts per year
var(mdata$cases)
[1] 915.5749
Quite a bit of over-dispersion here, so negative binomial distribution might be a better choice of distributional family than Poisson.
Fit the model with the data
prior_summary(m_pulmonary)
prior class coef group resp dpar nlpar lb ub source
normal(0, 1) b user
normal(0, 1) b acf_periodb.acf (vectorized)
normal(0, 1) b acf_periodc.postMacf (vectorized)
normal(0, 1) b y_num (vectorized)
normal(0, 1) b y_num:acf_periodb.acf (vectorized)
normal(0, 1) b y_num:acf_periodc.postMacf (vectorized)
normal(0, 1000) Intercept user
lkj_corr_cholesky(2) L user
lkj_corr_cholesky(2) L ward (vectorized)
exponential(1) sd 0 user
exponential(1) sd ward 0 (vectorized)
exponential(1) sd acf_periodb.acf ward 0 (vectorized)
exponential(1) sd acf_periodc.postMacf ward 0 (vectorized)
exponential(1) sd Intercept ward 0 (vectorized)
exponential(1) sd y_num ward 0 (vectorized)
exponential(1) sd y_num:acf_periodb.acf ward 0 (vectorized)
exponential(1) sd y_num:acf_periodc.postMacf ward 0 (vectorized)
gamma(0.01, 0.01) shape 0 user
Summarise the posterior in graphical form
Make this into a figure combined with the map of empirical data
ggsave(here("figures/f1.png"))
Saving 7 x 7 in image
Summary of change in notifications numerically
Numbers of pulmonary TB cases averted compared to counterfactual per year.
Total pulmonary TB cases averted between 1958 and 1963
What are the correlations between peak, level, and slope?
#RR.peak histogram
a <- overall_change$peak_draws %>%
ggplot() +
geom_histogram(aes(x=estimate), fill="darkblue", colour="darkblue", alpha=0.3)+
scale_fill_gradient(high="lightblue1",low="darkblue") +
theme_ggdist() +
theme(legend.position = "none",
panel.border = element_rect(colour = "grey78", fill=NA)) +
labs(x="RR.peak",
y="")
#RR. level histogram
b <- overall_change$level_draws %>%
ggplot() +
geom_histogram(aes(x=estimate), fill="darkblue", colour="darkblue", alpha=0.3)+
scale_fill_gradient(high="lightblue1",low="darkblue") +
theme_ggdist() +
theme(legend.position = "none",
panel.border = element_rect(colour = "grey78", fill=NA)) +
labs(x="RR.level",
y="")
#RR.slope histogram
c <- overall_change$slope_draws %>%
ggplot() +
geom_histogram(aes(x=estimate), fill="darkblue", colour="darkblue", alpha=0.3)+
scale_fill_gradient(high="lightblue1",low="darkblue") +
scale_x_continuous(limits = c(0, 6)) +
theme_ggdist() +
theme(legend.position = "none",
panel.border = element_rect(colour = "grey78", fill=NA)) +
labs(x="RR.slope",
y="")
#Correlation between RR.peak and RR.level
cor_rr_peak_rr_level <- round(cor(pluck(overall_change$peak_draws$estimate), pluck(overall_change$level_draws$estimate)), digits = 2)
#Correlation between RR.peak and RR.slope
cor_rr_peak_rr_slope <- round(cor(pluck(overall_change$peak_draws$estimate), pluck(overall_change$slope_draws$estimate)), digits = 2)
#Correlation between RR.level and RR.slope
cor_rr_level_rr_slope <- round(cor(pluck(overall_change$level_draws$estimate), pluck(overall_change$slope_draws$estimate)), digits = 2)
#plot of correlation between RR.peak and RR.level
d <- bind_cols(RR.peak=pluck(overall_change$peak_draws$estimate),
RR.level =pluck(overall_change$level_draws$estimate)) %>%
ggplot(aes(y=RR.peak, x = RR.level)) +
geom_hex() +
geom_smooth(se=FALSE, colour="firebrick", method = "lm") +
geom_text(aes(y=2.2, x=0.58, label=cor_rr_peak_rr_level), colour="firebrick") +
scale_fill_gradient(high="lightblue1",low="darkblue") +
theme_ggdist() +
theme(legend.position = "none",
panel.border = element_rect(colour = "grey78", fill=NA))
#plot of correlation between RR.peak and RR.slope
e <- bind_cols(RR.peak=pluck(overall_change$peak_draws$estimate),
RR.slope =pluck(overall_change$slope_draws$estimate)) %>%
ggplot(aes(y=RR.peak, x = RR.slope)) +
geom_hex() +
geom_smooth(se=FALSE, colour="firebrick") +
geom_text(aes(y=2.1, x=0.5, label=cor_rr_peak_rr_slope), colour="firebrick") +
scale_x_continuous(limits = c(0, 6)) +
scale_fill_gradient(high="lightblue1",low="darkblue") +
theme_ggdist() +
theme(legend.position = "none",
panel.border = element_rect(colour = "grey78", fill=NA))
#plot of correlation between RR.level and RR.slope
f <- bind_cols(RR.level=pluck(overall_change$level_draws$estimate),
RR.slope =pluck(overall_change$slope_draws$estimate)) %>%
ggplot(aes(y=RR.level, x = RR.slope)) +
geom_hex() +
geom_smooth(se=FALSE, colour="firebrick") +
geom_text(aes(y=0.75, x=0.5, label=cor_rr_level_rr_slope), colour="firebrick") +
scale_x_continuous(limits = c(0, 6)) +
scale_fill_gradient(high="lightblue1",low="darkblue") +
theme_ggdist() +
theme(legend.position = "none",
panel.border = element_rect(colour = "grey78", fill=NA))
(plot_spacer() + plot_spacer() + c) /
(plot_spacer() + b + f) /
(a + d + e)
ggsave(here("figures/pulmonary_cors.pdf"), width=8, height=8)
NA
NA
NA
Plot the counterfactual at ward level
Summary of change in notifications at ward level
ggsave(here("figures/s4.png"), width = 10)
Saving 10 x 7 in image
Calculate the counterfactual per ward
ward_pulmonary_counterf <- calculate_counterfactual(model_data = mdata, model=m_pulmonary,
population_denominator = population_without_inst_ship,
grouping_var = ward, re_formula=~(1 + y_num*acf_period | ward))
`summarise()` has grouped output by '.draw'. You can override using the `.groups` argument.`summarise()` has grouped output by '.draw'. You can override using the `.groups` argument.Joining with `by = join_by(year, population_without_inst_ship, .draw, ward)`Joining with `by = join_by(.draw, ward)`
ward_pulmonary_counterf$counter_post %>%
mutate(across(c(cases_averted:cases_averted.upper, diff_inc100k:diff_inc100k.upper), number_format(accuracy = 0.1, big.mark = ","))) %>%
mutate(across(c(rr_inc100k:rr_inc100k.upper), number_format(accuracy = 0.01))) %>%
mutate(across(c(pct_change:pct_change.upper), percent, accuracy=0.1)) %>%
datatable()
NA
NA
Overall counterfactual per ward
ward_pulmonary_counterf$counter_post_overall %>%
mutate(across(c(cases_averted:cases_averted.upper), number_format(accuracy = 0.1, big.mark = ","))) %>%
mutate(across(c(pct_change:pct_change.upper), percent, accuracy=0.1)) %>%
datatable()
NA
Now we will model the extra-pulmonary TB notification rate. Struggling a bit with negative binomial model, so revert to Poisson.
pp_check(m_extrapulmonary, type='ecdf_overlay')
Using 10 posterior draws for ppc type 'ecdf_overlay' by default.
Summarise in plot
Summarise numerically.
overall_change_extrapulmonary <- summarise_change(model_data=overall_scaffold, model=m_extrapulmonary,
population_denominator=population_without_inst_ship, grouping_var=NULL, re_formula = NA)
`summarise()` has grouped output by '.draw'. You can override using the `.groups` argument.
#want to keep the summary estimates here
tokeep <- c("peak_summary", "level_summary", "slope_summary")
#want to keep the summary estimates here
tokeep <- c("peak_summary", "level_summary", "slope_summary")
#summary measures in a table
overall_change_extrapulmonary %>%
keep((names(.) %in% tokeep)) %>%
bind_rows() %>%
mutate(across(c(estimate:.upper), number, accuracy=0.01)) %>%
select(measure, everything()) %>%
datatable
Numbers of extra-pulmonary TB cases averted overall.
Total extrapulmonary TB cases averted between 1958 and 1963
Ward-level extra-pulmonary estimates in graphical form.
Numerical summary.
Fit the model
(Not rewritten the functions for this yet)
m_age_sex <- brm(
cases ~ y_num + (acf_period)*(age*sex) + (acf_period:y_num)*(age*sex),
data = mdata_age_sex,
family = negbinomial(),
seed = 1234,
chains = 4, cores = 4,
prior = prior(normal(0,1000), class = Intercept) +
prior(gamma(0.01, 0.01), class = shape) +
prior(normal(0, 1), class = b))
Compiling Stan program...
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Summarise posterior
#posterior draws, and summarise
age_sex_summary <- mdata_age_sex %>%
select(year, year2, y_num, acf_period, age, sex) %>%
add_epred_draws(m_age_sex) %>%
group_by(year2, acf_period, age, sex) %>%
mean_qi() %>%
mutate(acf_period = case_when(acf_period=="a. pre-acf" ~ "Before Intervention",
acf_period=="c. post-acf" ~ "Post Intervention"))
#create the counterfactual (no intervention), and summarise
age_sex_counterfact <-
tibble(year = mdata_age_sex$year,
year2 = mdata_age_sex$year2,
y_num = mdata_age_sex$y_num,
age = mdata_age_sex$age,
sex = mdata_age_sex$sex,
acf_period = factor("a. pre-acf")) %>%
add_epred_draws(m_age_sex) %>%
group_by(year2, acf_period, age, sex) %>%
mean_qi() %>%
mutate(acf_period = case_when(acf_period=="a. pre-acf" ~ "Before Intervention",
acf_period=="c. post-acf" ~ "Post Intervention")) %>%
ungroup() %>%
mutate(age = case_when(age=="00_05" ~ "0 to 5y",
age=="06_15" ~ "06 to 15y",
age=="16_25" ~ "16 to 25y",
age=="26_35" ~ "26 to 35y",
age=="36_45" ~ "36 to 45y",
age=="46_55" ~ "46 to 55y",
age=="56_65" ~ "56 to 65y",
age=="65+" ~ "65 & up y")) %>%
mutate(sex = case_when(sex== "M" ~ "Male",
sex== "F" ~ "Female"))
age_sex_summary %>%
ungroup() %>%
mutate(age = case_when(age=="00_05" ~ "0 to 5y",
age=="06_15" ~ "06 to 15y",
age=="16_25" ~ "16 to 25y",
age=="26_35" ~ "26 to 35y",
age=="36_45" ~ "36 to 45y",
age=="46_55" ~ "46 to 55y",
age=="56_65" ~ "56 to 65y",
age=="65+" ~ "65 & up y")) %>%
mutate(sex = case_when(sex== "M" ~ "Male",
sex== "F" ~ "Female")) %>%
ggplot() +
geom_ribbon(aes(ymin=.epred.lower, ymax=.epred.upper, x=year2, group = acf_period, fill=acf_period), alpha=0.5) +
geom_ribbon(data = age_sex_counterfact %>% filter(year>=1956),
aes(ymin=.epred.lower, ymax=.epred.upper, x=year2, fill="Counterfactual"), alpha=0.5) +
geom_line(data = age_sex_counterfact %>% filter(year>=1956),
aes(y=.epred, x=year2, colour="Counterfactual")) +
geom_line(aes(y=.epred, x=year2, group=acf_period, colour=acf_period)) +
geom_point(data = mdata_age_sex %>%
ungroup() %>%
mutate(age = case_when(age=="00_05" ~ "0 to 5y",
age=="06_15" ~ "06 to 15y",
age=="16_25" ~ "16 to 25y",
age=="26_35" ~ "26 to 35y",
age=="36_45" ~ "36 to 45y",
age=="46_55" ~ "46 to 55y",
age=="56_65" ~ "56 to 65y",
age=="65+" ~ "65 & up y")) %>%
mutate(sex = case_when(sex== "M" ~ "Male",
sex== "F" ~ "Female")) , aes(y=cases, x=year2, shape=acf_period), size=2) +
geom_vline(aes(xintercept=acf_end), linetype=3) +
ggh4x::facet_grid2(age~sex, scales = "free_y", independent = "y") +
theme_ggdist() +
scale_y_continuous(labels=comma) +
scale_x_continuous(labels = year_labels,
breaks = year_labels,
guide = guide_axis(angle = 90)) +
scale_fill_manual(values = c("#DE0D92", "grey50", "#4D6CFA") , name="") +
scale_colour_manual(values = c("#DE0D92", "grey50", "#4D6CFA") , name="") +
scale_shape_discrete(name="") +
labs(
x = "Year",
y = "Case notifications (n)",
caption = "Mass miniature X-ray campaign period between dashed lines (11th March-12th April 1957)"
) +
theme(legend.position = "bottom",
panel.border = element_rect(colour = "grey78", fill=NA),
title = element_text(size=14),
axis.text = element_text(size=14),
legend.text = element_text(size=12)) +
guides(shape="none")
ggsave(here("figures/s7.png"), height=10)
Saving 7.29 x 10 in image
(This all needs tidying up and checking - to do!)
nd <- mdata_age_sex %>%
filter(year %in% c(1956:1957)) %>%
select(acf_period, y_num, age, sex)
age_sex_impact_out <-
add_epred_draws(m_age_sex,
newdata=nd) %>%
ungroup() %>%
select(acf_period, .epred, age, sex) %>%
pivot_wider(names_from = acf_period,
values_from = .epred,
values_fn = list) %>%
unnest() %>%
rename(pre_epred = 3,
post_epred = 4) %>%
mutate(acf_diff = post_epred-pre_epred,
acf_rr = post_epred/pre_epred) %>%
group_by(age, sex) %>%
mean_qi(acf_diff, acf_rr)
Warning: `cols` is now required when using `unnest()`.
ℹ Please use `cols = c(`a. pre-acf`, `b. acf`)`.
age_sex_impact_out %>%
mutate_if(is.double, ~ scales::number(x = ., accuracy = 0.01, big.mark = ",")) %>%
datatable()
`mutate_if()` ignored the following grouping variables:
f3a <- age_sex_impact_out %>%
mutate(sex = case_when(sex=="M" ~ "Male",
sex=="F" ~ "Female")) %>%
mutate(age = case_when(age=="00_05" ~ "0 to 5y",
age=="06_15" ~ "06 to 15y",
age=="16_25" ~ "16 to 25y",
age=="26_35" ~ "26 to 35y",
age=="36_45" ~ "36 to 45y",
age=="46_55" ~ "46 to 55y",
age=="56_65" ~ "56 to 65y",
age=="65+" ~ "65 & up y")) %>%
ggplot() +
geom_pointrange(aes(y=acf_rr, ymin=acf_rr.lower, ymax=acf_rr.upper, group=sex,
x=age,
colour = sex),
position = position_dodge(width = 0.25)) +
geom_hline(aes(yintercept=1), linetype=2) +
scale_colour_manual(values = c("purple", "darkorange"), name="") +
labs(x="",
y="Relative notifications (95% UI)\nACF (1957) vs. Before ACF (1956)") +
theme_ggdist() +
theme(legend.position = "bottom",
panel.border = element_rect(colour = "grey78", fill=NA))
nd <- mdata_age_sex %>%
filter(year %in% c(1956,1958)) %>%
select(acf_period, y_num, age, sex)
#Do it with calculating incidence, then sumamrising.
age_sex_impact2 <-add_epred_draws(m_age_sex,
newdata=nd) %>%
ungroup() %>%
select(acf_period, .epred, age, sex) %>%
pivot_wider(names_from = acf_period,
values_from = .epred,
values_fn = list) %>%
unnest() %>%
rename(pre_epred = 3,
post_epred = 4) %>%
mutate(acf_diff = post_epred-pre_epred,
acf_rr = post_epred/pre_epred) %>%
group_by(age, sex) %>%
mean_qi(acf_diff, acf_rr)
Warning: `cols` is now required when using `unnest()`.
ℹ Please use `cols = c(`a. pre-acf`, `c. post-acf`)`.
age_sex_impact2 %>%
mutate_if(is.double, ~ scales::number(x = ., accuracy = 0.01, big.mark = ",")) %>%
datatable()
`mutate_if()` ignored the following grouping variables:
f3b <- age_sex_impact2 %>%
mutate(sex = case_when(sex=="M" ~ "Male",
sex=="F" ~ "Female")) %>%
mutate(age = case_when(age=="00_05" ~ "0 to 5y",
age=="06_15" ~ "06 to 15y",
age=="16_25" ~ "16 to 25y",
age=="26_35" ~ "26 to 35y",
age=="36_45" ~ "36 to 45y",
age=="46_55" ~ "46 to 55y",
age=="56_65" ~ "56 to 65y",
age=="65+" ~ "65 & up y")) %>%
ggplot() +
geom_pointrange(aes(y=acf_rr, ymin=acf_rr.lower, ymax=acf_rr.upper, group=sex,
x=age,
colour = sex),
position = position_dodge(width = 0.25)) +
geom_hline(aes(yintercept=1), linetype=2) +
scale_colour_manual(values = c("purple", "darkorange"), name="") +
labs(x="",
y="Relative notifications (95% UI)\nACF (1958) vs. Before ACF (1956)") +
theme_ggdist() +
theme(legend.position = "bottom",
panel.border = element_rect(colour = "grey78", fill=NA))
age_sex_impact3 <- mdata_age_sex %>%
select(year, year2, y_num, acf_period, cases, age, sex) %>%
filter(year!=1957) %>%
add_epred_draws(m_age_sex) %>%
group_by(year, age, sex, acf_period) %>%
mean_qi(.epred) %>%
ungroup() %>%
mutate(n_years = length(year), .by=acf_period) %>%
summarise(pct_change_epred_overall = (((last(.epred) - first(.epred))/first(.epred))),
pct_change_lower_overall = (((last(.lower) - first(.lower))/first(.lower))),
pct_change_upper_overall = (((last(.upper) - first(.upper))/first(.upper))),
pct_change_epred_annual = (((last(.epred) - first(.epred))/first(.epred))/n_years),
pct_change_lower_annual = (((last(.lower) - first(.lower))/first(.lower))/n_years),
pct_change_upper_annual = (((last(.upper) - first(.upper))/first(.upper))/n_years),
.by = c(acf_period, age, sex)) %>%
distinct()
Warning: Returning more (or less) than 1 row per `summarise()` group was deprecated in dplyr 1.1.0.
Please use `reframe()` instead.
When switching from `summarise()` to `reframe()`, remember that `reframe()` always returns an ungrouped data frame and adjust accordingly.
age_sex_impact3 %>%
mutate_if(is.double, percent) %>%
datatable()
f3c <- age_sex_impact3 %>%
mutate(sex = case_when(sex=="M" ~ "Male",
sex=="F" ~ "Female")) %>%
mutate(age = case_when(age=="00_05" ~ "0 to 5y",
age=="06_15" ~ "06 to 15y",
age=="16_25" ~ "16 to 25y",
age=="26_35" ~ "26 to 35y",
age=="36_45" ~ "36 to 45y",
age=="46_55" ~ "46 to 55y",
age=="56_65" ~ "56 to 65y",
age=="65+" ~ "65 & up y")) %>%
ggplot() +
geom_hline(aes(yintercept=0), linetype=2) +
geom_pointrange(aes(y=pct_change_epred_annual, ymin=pct_change_lower_annual, ymax=pct_change_upper_annual, group=acf_period,
x=age,
colour = acf_period), size=0.1) +
scale_y_continuous(labels =percent) +
facet_grid(.~sex) +
coord_flip() +
scale_colour_manual(values = c("#DE0D92", "#4D6CFA")) +
labs(x="",
y="Mean annual rate of change in case notification rate (95% UI)\n Before ACF (1950-1956) vs. after ACF (1958-1963)",
colour="") +
theme_ggdist() +
theme(panel.border = element_rect(colour = "grey78", fill=NA))
f3c
counterfact_age_sex <-
add_epred_draws(object = m_age_sex,
newdata = mdata_age_sex %>%
select(year, year2, y_num, age, sex) %>%
mutate(acf_period = "a. pre-acf")) %>%
filter(year>1957) %>%
select(year, age, sex, .draw, .epred_counterf = .epred)
Adding missing grouping variables: `year2`, `y_num`, `acf_period`, `.row`
#Calcuate incidence per draw, then summarise.
post_change_age_sex <-
add_epred_draws(object = m_age_sex,
newdata = mdata_age_sex %>%
select(year, year2, y_num, age, sex, acf_period)) %>%
filter(year>1957) %>%
ungroup() %>%
select(year, age, sex, .draw, .epred)
#for the overall period
counterfact_overall_age_sex <-
add_epred_draws(object = m_age_sex,
newdata = mdata_age_sex %>%
select(year, year2, y_num, age, sex) %>%
mutate(acf_period = "a. pre-acf")) %>%
filter(year>1957) %>%
select(age, sex, .draw, .epred) %>%
group_by(age, sex, .draw) %>%
summarise(.epred_counterf = sum(.epred)) %>%
mutate(year = "Overall (1958-1963)")
Adding missing grouping variables: `year`, `year2`, `y_num`, `acf_period`, `.row``summarise()` has grouped output by 'age', 'sex'. You can override using the `.groups` argument.
#Calcuate incidence per draw, then summarise.
post_change_overall_age_sex <-
add_epred_draws(object = m_age_sex,
newdata = mdata_age_sex %>%
select(year, year2, y_num, age, sex, acf_period)) %>%
filter(year>1957) %>%
select(age, sex, .draw, .epred) %>%
group_by(.draw, age, sex) %>%
summarise(.epred = sum(.epred))
Adding missing grouping variables: `year`, `year2`, `y_num`, `acf_period`, `.row``summarise()` has grouped output by '.draw', 'age'. You can override using the `.groups` argument.
left_join(counterfact_age_sex, post_change_age_sex) %>%
mutate(cases_averted = .epred_counterf-.epred,
pct_change = (.epred - .epred_counterf)/.epred_counterf) %>%
group_by(year, age, sex) %>%
mean_qi(cases_averted, pct_change) %>%
ungroup() %>%
datatable()
Joining with `by = join_by(year, age, sex, .draw)`
counter_post_overall_age_sex <-
left_join(counterfact_overall_age_sex, post_change_overall_age_sex) %>%
mutate(cases_averted = .epred_counterf-.epred,
pct_change = (.epred - .epred_counterf)/.epred_counterf) %>%
group_by(age, sex) %>%
mean_qi(cases_averted, pct_change) %>%
ungroup() %>%
mutate(year = "Overall (1958-1963)")
Joining with `by = join_by(age, sex, .draw)`
age_sex_txt <- counter_post_overall_age_sex %>%
mutate(across(c(cases_averted:cases_averted.upper), number_format(accuracy = 0.1, big.mark = ","))) %>%
mutate(across(c(pct_change:pct_change.upper), percent, accuracy=0.1)) %>%
transmute(year = as.character(year),
sex = sex,
age = age,
cases_averted = glue::glue("{cases_averted}\n({cases_averted.lower} to {cases_averted.upper})"),
pct_change = glue::glue("{pct_change}\n({pct_change.lower} to {pct_change.upper})"))
age_sex_txt %>% datatable()
NA
NA
f3d <- counter_post_overall_age_sex %>%
mutate(sex = case_when(sex=="M" ~ "Male",
sex=="F" ~ "Female")) %>%
mutate(age = case_when(age=="00_05" ~ "0 to 5y",
age=="06_15" ~ "06 to 15y",
age=="16_25" ~ "16 to 25y",
age=="26_35" ~ "26 to 35y",
age=="36_45" ~ "36 to 45y",
age=="46_55" ~ "46 to 55y",
age=="56_65" ~ "56 to 65y",
age=="65+" ~ "65 & up y")) %>%
ggplot() +
geom_pointrange(aes(x = age, y=cases_averted, ymin=cases_averted.lower, ymax=cases_averted.upper, colour=sex)) +
facet_grid(.~sex) +
coord_flip() +
scale_colour_manual(values = c("purple", "darkorange"), name="") +
scale_y_continuous(labels = comma) +
labs(x="",
y="Number (95% UI) of TB cases averted (1958-1963)",
colour="") +
theme_ggdist() +
theme(panel.border = element_rect(colour = "grey78", fill=NA),
legend.position = "none")
f3d
Join together for Figure 2.
(f3a + f3b) / (f3c + f3d) + plot_annotation(tag_levels = "A")
ggsave(here("figures/f3.png"), width = 12)
Saving 12 x 4.51 in image
mdata_age_sex